MNE_MRI_preprocessing
Before starting the Freesurfer analysis, you have to set some "environment variables", so that the following processing scripts know where to look for programs and data.
Type
freesurfer_4.3.0 and setenv SUBJECTS_DIR </myMRIdirectory/>
in your Linux command window.
Freesurfer will create a number of files in several subdirectories for each subject. You can automatically create the subdirecties for each subject
mksubjdirs <mysubjectname>
This will create the directory /myMRIdirectory/mysubjectname/, as well as several subdirectories. Check whether it worked, then forget about it for the time being.